Ubuntu – Prompt overwrite file in echo

The main problem is here:

read $input

In bash, usually, $foo is the value of the variable foo. Here, you don't want the value, but the name of the variable, so it should be just:

read input

Similarly, in the if tests, $yes and $no should be just yes and no, since you just want the strings yes and no there.

You could use a case statement here, which (IMHO) makes it easier to do multiple cases based on input:

case $input in
[Yy]es)    # The first character can be Y or y, so both Yes and yes work
    echo "Hello!"  
    echo "Hello!" | festival --tts
    ;;
[Nn]o)     # no or No
    echo "Are you sure?"
    echo "Are you sure?" | festival --tts
    ;;
*)         # Anything else
    echo "Please answer yes or no."
    echo "Please answer yes or no." | festival --tts
    ;;
esac

You could wrap the two echo statements and the use of festival in a function to avoid repeating yourself:

textAndSpeech ()
{
    echo "$@"
    echo "$@" | festival --tts
}
case $input in
[Yy]es)    # The first character can be Y or y, so both Yes and yes work
    textAndSpeech "Hello!"  
    ;;
[Nn]o)     # no or No
    textAndSpeech "Are you sure?"
    ;;
*)         # Anything else
    textAndSpeech "Please answer yes or no."
    ;;
esac

With $input, bash replaces this with its value, which is nothing initially, so the read command run is:

read 

And read by default stores the input in the variable REPLY. So you can, if you want, eliminate the input variable altogether and use $REPLY instead of $input.

Also have a look at the select statement in Bash.

If one really really really needs to have custom cp with custom message, then recompiling the program from source is the way to go, but a bit more sensible approach would be to write out your own message via printf preferably, instead of trying to intercept cp's output, and handle user choices via select dialog. Additionally, if you're going to output error messages, they should go to stderr stream. Finally, *.* is unnecessary and you can just use * glob instead.

Below is the script with a couple edits. Note that you need to uncomment #cp "$item" "$HOMEWORKDIRECTORY" line for the actual copying to occur. For testing purposes replace cp with echo first.

#!/bin/bash

USAGE="Usage: ./script2.sh [hw-name]"
EINVALID="Invalid homework: $1"
SOURCEDIRECTORY="$PUBLIC/homework/$1"
HOMEWORKDIRECTORY="$HOME/homework/$1"
#COPY="$SOURCEDIRECTORY/*.*"

if [ -z "$1" ]; then
    echo "$USAGE" > /dev/stderr
    exit 1
fi

if [ ! -d "$SOURCEDIRECTORY" ]; then
    echo "$EINVALID" > /dev/stderr
    exit 2
fi

if [ ! -d "$HOMEWORKDIRECTORY" ]; then
    echo "making homework1"
    mkdir -p $HOMEWORKDIRECTORY

for item in "$SOURCEDIRECTORY"/*; do
    skip=true
    if [ -f "$HOMEWORKDIRECTORY"/"${item##*/}" ]; then
        printf "%s already exists in %s.\n" "$item" "$HOMEWORKDIRECTORY"

        select choice in  "overwrite" "skip"; do
            case "$choice" in 
                "overwrite")  echo "Overwriting."  
                              break;;
                "skip") skip=true; break;;
            esac
        done
    fi

    if [ "$skip" = "true" ]; then
        continue
    fi
    echo cp "$item" "$HOMEWORKDIRECTORY"

done